amino acid pair
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2021 ◽  
Vol 2021 ◽  
pp. 1-7
Author(s):  
Shujun Shan ◽  
Yue Qi ◽  
Jihong Jiang ◽  
Song Guo

Ubiquitin is an important type of protein after translational modification. Ubiquitin has the ability to take part in several cellular regulations among several biological processions. At the same time, ubiquitin plays key roles in the enzymatic process. So as to construct the new tool to classify the ubiquitin amino acid residues, we employed the random forest model to classify the ubiquitin sites utilizing the experimentally identified ubiquitinated protein sequences of A. thaliana. More detailed, we utilized the k-spaced amino acid pair (CKSAAP) encoding and binary encoding to deal with the potential protein segments. The proposed tools can obtain 72.83% in Sp, 72.42% in Sn, 72.63% in Acc, and 0.4525 in MCC. With these performances, such tools can obtain the available results in the dataset of Arabidopsis.


2020 ◽  
Vol 18 (21) ◽  
pp. 4079-4084
Author(s):  
Patrick R. Gleason ◽  
Patrick I. Kelly ◽  
Dominic W. Grisingher ◽  
Jeremy H. Mills

The non-canonical amino acid l-(7-hydroxycoumarin-4-yl)ethylglycine can serve as a FRET acceptor from tryptophan. Here, we demonstrate how this amino acid pair can be used to generate an intrinsic FRET-based sensor of protein–ligand interactions.


2019 ◽  
Vol 21 (24) ◽  
pp. 12843-12849 ◽  
Author(s):  
Ismail A. Ahmed ◽  
Jeffrey M. Rodgers ◽  
Christina Eng ◽  
Thomas Troxler ◽  
Feng Gai

The amino acids tryptophan and 4-cyanotryptophan constitute a dual FRET and PET pair, useful for various biological applications.


2018 ◽  
Vol 17 (4) ◽  
pp. 394-401 ◽  
Author(s):  
Yan Xu ◽  
Yingxi Yang ◽  
Jun Ding ◽  
Chunhui Li
Keyword(s):  

PLoS ONE ◽  
2012 ◽  
Vol 7 (7) ◽  
pp. e41322 ◽  
Author(s):  
Steffen B. Petersen ◽  
Maria Teresa Neves-Petersen ◽  
Svend B. Henriksen ◽  
Rasmus J. Mortensen ◽  
Henrik M. Geertz-Hansen

2012 ◽  
Vol 287 (23) ◽  
pp. 19674-19686 ◽  
Author(s):  
Miguel Álvaro-Benito ◽  
M. Angela Sainz-Polo ◽  
David González-Pérez ◽  
Beatriz González ◽  
Francisco J. Plou ◽  
...  
Keyword(s):  

PLoS ONE ◽  
2011 ◽  
Vol 6 (12) ◽  
pp. e25638 ◽  
Author(s):  
Svend B. Henriksen ◽  
Rasmus J. Mortensen ◽  
Henrik M. Geertz-Hansen ◽  
Maria Teresa Neves-Petersen ◽  
Omar Arnason ◽  
...  
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